Start with at least a 100 amp alternator and 3-4 deep cycle marine batteries that are isolated from your starting and house load batteries and feed only the amps. You are looking at well over a thousand watts for everything. Run a massive main power wire and ground wire up to the amp location and get some serious distribution blocks.
3 amps, 1 for the cabin speakers, 1 for the subs, 1 for the tower. Opinions will vary as to the wattages you need. Look into an EQ that can adjust the levels for three amps, then you can control your tower, cabin, and subs seperately. You could also use the fader on the head unit for this as well, but you will only have 2 channels of control.
You could simplify and use only one sub and maybe get a 6 channel amp and bridge 2 channels for the sub and use the other 4 for the cabin. Something like the JL e6450 would work nice, it puts out more than it's rated power. Use the Clarion for your tower and see how you like it, you can always upgrade it. This setup would keep you right around a thousand watts and you could use 2 isolated batteries. You still should have a 100 amp alternator though or you will be draining batteries quickly.
Do a search here, there are a ton of nice setups that people have posted pictures of.